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Nucleic Acids Research 2006 34(Web Server issue):W645-W650; doi:10.1093/nar/gkl229
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

Applications for protein sequence–function evolution data: mRNA/protein expression analysis and coding SNP scoring tools

Paul D. Thomas*, Anish Kejariwal, Nan Guo, Huaiyu Mi, Michael J. Campbell, Anushya Muruganujan and Betty Lazareva-Ulitsky

Evolutionary Systems Biology Group, SRI International 333 Ravenswood Ave., Menlo Park CA 94025, USA

*To whom correspondence should be addressed. Tel: +1 650 859 2434; Fax: +1 650 859 3735; Email: paul.thomas{at}sri.com

Received February 14, 2006. Revised March 6, 2006. Accepted March 27, 2006.

The vast amount of protein sequence data now available, together with accumulating experimental knowledge of protein function, enables modeling of protein sequence and function evolution. The PANTHER database was designed to model evolutionary sequence–function relationships on a large scale. There are a number of applications for these data, and we have implemented web services that address three of them. The first is a protein classification service. Proteins can be classified, using only their amino acid sequences, to evolutionary groups at both the family and subfamily levels. Specific subfamilies, and often families, are further classified when possible according to their functions, including molecular function and the biological processes and pathways they participate in. The second application, then, is an expression data analysis service, where functional classification information can help find biological patterns in the data obtained from genome-wide experiments. The third application is a coding single-nucleotide polymorphism scoring service. In this case, information about evolutionarily related proteins is used to assess the likelihood of a deleterious effect on protein function arising from a single substitution at a specific amino acid position in the protein. All three web services are available at http://www.pantherdb.org/tools.


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